2022
Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1
Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Rolon R, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, Initiative Y, Rhoads DD. Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. Journal Of Clinical Microbiology 2022, 60: e00600-22. PMID: 35582905, PMCID: PMC9199403, DOI: 10.1128/jcm.00600-22.Peer-Reviewed Original Research
2021
Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity
Lucas C, Vogels CBF, Yildirim I, Rothman JE, Lu P, Monteiro V, Gehlhausen JR, Campbell M, Silva J, Tabachnikova A, Peña-Hernandez MA, Muenker MC, Breban MI, Fauver JR, Mohanty S, Huang J, Shaw A, Ko A, Omer S, Grubaugh N, Iwasaki A. Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity. Nature 2021, 600: 523-529. PMID: 34634791, PMCID: PMC9348899, DOI: 10.1038/s41586-021-04085-y.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 variantsMRNA vaccine-induced immunityT-cell activation markersSARS-CoV-2 antibodiesSecond vaccine doseVaccine-induced immunityCell activation markersT cell responsesHigh antibody titresSARS-CoV-2Vaccine boosterVaccine doseActivation markersVaccine dosesHumoral immunityAntibody titresMRNA vaccinesVitro stimulationNeutralization capacityNeutralization responseCell responsesE484KNucleocapsid peptideAntibody-binding sitesGreater reductionCOVID-19 vaccines: Keeping pace with SARS-CoV-2 variants
Cevik M, Grubaugh ND, Iwasaki A, Openshaw P. COVID-19 vaccines: Keeping pace with SARS-CoV-2 variants. Cell 2021, 184: 5077-5081. PMID: 34534444, PMCID: PMC8445744, DOI: 10.1016/j.cell.2021.09.010.Peer-Reviewed Original ResearchMultiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, de Jesus J, Claro I, Ferreira G, Crispim MAE, Network B, Singh L, Tegally H, Anyaneji UJ, Africa N, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLOS Biology 2021, 19: e3001236. PMID: 33961632, PMCID: PMC8133773, DOI: 10.1371/journal.pbio.3001236.Peer-Reviewed Original Research
2020
Two Sides of a Coin: a Zika Virus Mutation Selected in Pregnant Rhesus Macaques Promotes Fetal Infection in Mice but at a Cost of Reduced Fitness in Nonpregnant Macaques and Diminished Transmissibility by Vectors
Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Martin CS, Li T, Martyn C, Oliveira G, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY, Van Rompay KKA, Coffey LL. Two Sides of a Coin: a Zika Virus Mutation Selected in Pregnant Rhesus Macaques Promotes Fetal Infection in Mice but at a Cost of Reduced Fitness in Nonpregnant Macaques and Diminished Transmissibility by Vectors. Journal Of Virology 2020, 94: 10.1128/jvi.01605-20. PMID: 32999034, PMCID: PMC7925200, DOI: 10.1128/jvi.01605-20.Peer-Reviewed Original ResearchConceptsCongenital Zika syndromeZika virusFetal infectionFetal deathZika syndromePregnant micePregnant wild-type miceRhesus macaque fetusesPregnant rhesus macaquesZika virus infectionWild-type miceNonpregnant hostsPlacental infectionLow viremiaMajority of animalsPregnant womenPregnant macaquesSevere outcomesMacaque fetusesVirus infectionFetusesInfectionZIKV polyproteinMouse fetusesRhesus macaquesMaking sense of mutation: what D614G means for the COVID-19 pandemic remains unclear
Grubaugh ND, Hanage WP, Rasmussen AL. Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear. Cell 2020, 182: 794-795. PMID: 32697970, PMCID: PMC7332445, DOI: 10.1016/j.cell.2020.06.040.Peer-Reviewed Original ResearchWe shouldn’t worry when a virus mutates during disease outbreaks
Grubaugh ND, Petrone ME, Holmes EC. We shouldn’t worry when a virus mutates during disease outbreaks. Nature Microbiology 2020, 5: 529-530. PMID: 32071422, PMCID: PMC7095397, DOI: 10.1038/s41564-020-0690-4.Peer-Reviewed Original Research
2019
Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts
Scroggs SLP, Grubaugh ND, Sena JA, Sundararajan A, Schilkey FD, Smith DR, Ebel GD, Hanley KA. Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts. MSphere 2019, 4: 10.1128/msphere.00291-19. PMID: 31243074, PMCID: PMC6595145, DOI: 10.1128/msphere.00291-19.Peer-Reviewed Original ResearchConceptsUntranslated regionSecondary structureBird speciesRNA genomeGenome cyclizationRNA virusesHost variationPrimary genomic sequenceWest Nile virusPrimary genome sequenceDS regionStructural diversityIntrahost genetic diversityVirus phenotypeComplex secondary structureVirus RNA genomeRNA secondary structureSerial passageSmall RNAsGenetic diversityNile virusGenome sequenceMutant lineagesGenomic sequencesNext-generation sequencingMisperceived Risks of Zika-related Microcephaly in India
Grubaugh ND, Ishtiaq F, Setoh YX, Ko AI. Misperceived Risks of Zika-related Microcephaly in India. Trends In Microbiology 2019, 27: 381-383. PMID: 30826180, DOI: 10.1016/j.tim.2019.02.004.Peer-Reviewed Original Research
2017
Zika virus evolution and spread in the Americas
Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC. Zika virus evolution and spread in the Americas. Nature 2017, 546: 411-415. PMID: 28538734, PMCID: PMC5563848, DOI: 10.1038/nature22402.Peer-Reviewed Original Research
2016
Genetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host Switching
Grubaugh ND, Weger-Lucarelli J, Murrieta RA, Fauver JR, Garcia-Luna SM, Prasad AN, Black WC, Ebel GD. Genetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host Switching. Cell Host & Microbe 2016, 19: 481-492. PMID: 27049584, PMCID: PMC4833525, DOI: 10.1016/j.chom.2016.03.002.Peer-Reviewed Original ResearchConceptsRelative fitnessMosquito speciesLower relative fitnessWest Nile virusComplex virus populationsSignificant fitness costMosquito-borne RNA virusesHost switchingGenetic driftGenetic diversityAdaptive potentialPopulation expansionFitness costsAvian cellsDeleterious mutationsMutational diversityRNA virusesBridge vectorsViral populationsVirus populationsMosquito vectorsFitnessSpeciesDiversityNile virus
2015
Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness
Grubaugh ND, Smith DR, Brackney DE, Bosco-Lauth AM, Fauver JR, Campbell CL, Felix TA, Romo H, Duggal NK, Dietrich EA, Eike T, Beane JE, Bowen RA, Black WC, Brault AC, Ebel GD. Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness. PLOS Pathogens 2015, 11: e1004874. PMID: 25993022, PMCID: PMC4439088, DOI: 10.1371/journal.ppat.1004874.Peer-Reviewed Original ResearchConceptsRNA virus populationsWNV populationsBird speciesRNA virusesNatural selectionFitness gainsVirus populationsStrength of selectionWest Nile virusSpecies-specific mannerDistinct phenotypic consequencesAverage mutation frequencyExperimental evolutionMutational toleranceError-prone replicationCompetitive fitnessPopulation structureNext-generation sequencingPhenotypic consequencesGenetic compositionWild birdsSelective pressureSequencing dataDefective genomesDifferent hosts